scPDB - 4xbf entry

Protein Data Bank Entry:

PDB ID : 4xbf

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2014-12-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysine-specific histone demethylase 1A
ID:	KDM1A_HUMAN
AC:	O60341
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	35.510
Number of residues:	66
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.347	789.750

% Hydrophobic	% Polar
53.42	46.58
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	78.37 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
187.996	65.8349	30.6205

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O1P	OG	SER- 289	2.69	151.72	H-Bond (Protein Donor)	false
O1P	N	SER- 289	3.12	155.2	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 308	2.52	152.72	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 308	2.9	123.36	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 308	2.66	172.42	H-Bond (Ligand Donor)	false
N3A	N	ALA- 309	3.3	132.45	H-Bond (Protein Donor)	false
O1A	NE	ARG- 316	2.9	156.84	H-Bond (Protein Donor)	false
O2A	N	ARG- 316	2.88	170.26	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 316	2.94	146	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 316	3.68	0	Ionic (Protein Cationic)	false
C8M	CD	ARG- 316	4.1	0	Hydrophobic	false
C3'	CB	ARG- 316	4.14	0	Hydrophobic	false
C9A	CB	ALA- 331	4.35	0	Hydrophobic	false
C2'	CB	ALA- 331	4.24	0	Hydrophobic	false
O4	N	MET- 332	3.37	160.07	H-Bond (Protein Donor)	false
N3	O	VAL- 333	2.65	135.7	H-Bond (Ligand Donor)	false
O4	N	VAL- 333	2.81	155.17	H-Bond (Protein Donor)	false
N6A	O	VAL- 590	3.07	162.29	H-Bond (Ligand Donor)	false
N1A	N	VAL- 590	3.03	142.34	H-Bond (Protein Donor)	false
C5B	CG2	THR- 624	3.79	0	Hydrophobic	false
C5B	CG	PRO- 626	4.05	0	Hydrophobic	false
C7M	CD1	LEU- 659	3.72	0	Hydrophobic	false
C7M	CE2	TRP- 751	4.24	0	Hydrophobic	false
C8M	CD2	TRP- 751	4.04	0	Hydrophobic	false
C2B	CB	TRP- 756	3.95	0	Hydrophobic	false
C8M	CB	SER- 760	3.31	0	Hydrophobic	false
C8M	CD2	TYR- 761	4.46	0	Hydrophobic	false
C1'	CD2	TYR- 761	3.91	0	Hydrophobic	false
C9	CD2	TYR- 761	3.4	0	Hydrophobic	false
C5'	CB	GLU- 801	4.04	0	Hydrophobic	false
O2P	N	GLU- 801	2.78	162.4	H-Bond (Protein Donor)	false
O2	N	VAL- 811	3.09	166.6	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 811	3.67	0	Hydrophobic	false
C4'	CG2	VAL- 811	4.26	0	Hydrophobic	false
C5'	CB	ALA- 814	3.92	0	Hydrophobic	false
O4'	O	HOH- 1004	2.73	173.65	H-Bond (Ligand Donor)	false
O1A	O	HOH- 1015	2.8	156.1	H-Bond (Protein Donor)	false
O1P	O	HOH- 1016	3.29	167.86	H-Bond (Protein Donor)	false